From 1521e764c37d73132e58fb454850715c046af8c3 Mon Sep 17 00:00:00 2001
From: Andrey Kislyuk <weaver@gentoo.org>
Date: Sun, 25 Jan 2009 19:33:17 +0000
Subject: Import dev-java/biojava and dependencies from Java overlay, thanks to
 serkan (Portage version: 2.2_rc20/cvs/Linux 2.6.26-gentoo-r4 x86_64)

---
 dev-java/biojava/ChangeLog          | 13 +++++++
 dev-java/biojava/biojava-1.6.ebuild | 73 +++++++++++++++++++++++++++++++++++++
 dev-java/biojava/metadata.xml       |  6 +++
 3 files changed, 92 insertions(+)
 create mode 100644 dev-java/biojava/ChangeLog
 create mode 100644 dev-java/biojava/biojava-1.6.ebuild
 create mode 100644 dev-java/biojava/metadata.xml

(limited to 'dev-java/biojava')

diff --git a/dev-java/biojava/ChangeLog b/dev-java/biojava/ChangeLog
new file mode 100644
index 000000000000..3d4eb760f58d
--- /dev/null
+++ b/dev-java/biojava/ChangeLog
@@ -0,0 +1,13 @@
+# ChangeLog for dev-java/biojava
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/dev-java/biojava/ChangeLog,v 1.1 2009/01/25 19:33:17 weaver Exp $
+
+*biojava-1.6 (25 Jan 2009)
+
+  25 Jan 2009; weaver <weaver@gentoo.org> +metadata.xml,
+  +biojava-1.6.ebuild:
+  Import from Java overlay, thanks to serkan
+
+  22 Jan 2009; Alistair Bush <ali_bush@gentoo.org> ChangeLog:
+  Add ChangeLog for QA.
+
diff --git a/dev-java/biojava/biojava-1.6.ebuild b/dev-java/biojava/biojava-1.6.ebuild
new file mode 100644
index 000000000000..0db0b2efb96f
--- /dev/null
+++ b/dev-java/biojava/biojava-1.6.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/dev-java/biojava/biojava-1.6.ebuild,v 1.1 2009/01/25 19:33:17 weaver Exp $
+
+# TODO:
+# -Fix javadoc generation OutOfMemoryError
+# -Add launchers for 2 apps in biojava-apps.jar
+# -Decide on demo packaging. (Whether to install its jar as done or sources by examples USE flag)
+
+EAPI=2
+
+#JAVA_PKG_IUSE="doc source test"
+JAVA_PKG_IUSE="source test"
+
+inherit eutils java-pkg-2 java-ant-2
+
+DESCRIPTION="A Java framework for processing biological data"
+HOMEPAGE="http://biojava.org"
+SRC_URI="http://www.biojava.org/download/bj16/all/${P}-all.jar"
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+COMMON_DEPEND="dev-java/jgrapht:0
+	dev-java/commons-cli:1
+	dev-java/commons-dbcp:0
+	dev-java/commons-pool:0
+	dev-java/bytecode:0"
+
+RDEPEND=">=virtual/jre-1.5
+	${COMMON_DEPEND}"
+DEPEND=">=virtual/jdk-1.5
+	app-arch/unzip
+	${COMMON_DEPEND}
+	test?
+	(
+		dev-java/junit:4
+		dev-java/ant-junit4
+	)"
+
+S="${WORKDIR}/biojava-live_${PV}"
+
+JAVA_ANT_IGNORE_SYSTEM_CLASSES="true"
+
+src_prepare() {
+	einfo "Removing budled jars."
+	find . -name "*.jar" -print -delete
+	rm -r doc/*
+	java-pkg_jar-from jgrapht jgrapht.jar jgrapht-jdk1.5.jar
+	java-pkg_jar-from commons-cli-1
+	java-pkg_jar-from commons-dbcp commons-dbcp.jar commons-dbcp-1.1.jar
+	java-pkg_jar-from commons-pool commons-pool.jar commons-pool-1.1.jar
+	java-pkg_jar-from bytecode
+}
+
+src_compile() {
+	#ANT_OPTS="${ANT_OPTS} -Xmx512m"
+	eant package-biojava package-biojava package-demos package-apps #$(use_doc javadocs-all)
+}
+
+src_install() {
+	java-pkg_newjar ant-build/biojava.jar ${PN}.jar
+	java-pkg_newjar ant-build/apps.jar ${PN}-apps.jar
+	java-pkg_newjar ant-build/demos.jar ${PN}-demos.jar
+	#use doc && java-pkg_dojavadoc ant-build/doc/{biojava,apps,demos}
+	use source && java-pkg_dosrc {src,apps,demos}/org
+}
+
+src_test() {
+	java-pkg_jar-from junit-4 junit.jar junit-4.4.jar
+	ANT_TASKS="ant-junit4" eant runtests
+}
diff --git a/dev-java/biojava/metadata.xml b/dev-java/biojava/metadata.xml
new file mode 100644
index 000000000000..604e0a4238bb
--- /dev/null
+++ b/dev-java/biojava/metadata.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>java</herd>
+</pkgmetadata>
+
-- 
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